I voted for Cyclok, Diabolical Cubus Sisters, and Gleeok.
Cyclok was honestly one of my favorite bosses, because he's not too hard, and not too easy. It took me a little bit to figure out what to do, but using the wind to lift the bomb up was a unique idea!
At first, I thought that the Diabolical Cubus Sisters were just nice girls who needed help, but I surely was wrong! It was kinda cool to play volleyball with them with your sword to defeat them, so yeah...
The strategy to defeat Gleeok was really unique and it did take me a while to find out what to do, since, I used cheat codes on the first time through Phantom Hourglass (Hey, I didn't know that it would be super easy!) and I just jumped the whole way to the boss.